Membrane bioreactor-reverse osmosis process (MBR-RO) is widely applied in wastewater treatment, especially when high-quality treated water is needed. Although MBR shows better performances in the removal of pathogens than the conventional activated sludge process, stable operation of RO process in the latter step of MBR-RO depends on residual bacteria in the filtrate of microfiltration membranes. Species and sizes of bacteria found in the filtrate of activated sludge with 0.2 μm poresize polycarbonate membranes were investigated in this study. Isolated bacterial species grown on R2A agar medium were identified based on the full length 16S rRNA gene sequences. The result showed that approximately 90% of the isolates found in the filtrates were members of phylum Proteobacteria in which Ralstonia spp., Achromobacter spp., Methylobacterium spp. and Methylorubrum spp. accounted for the largest proportions while other bacteria affiliated with phyla Actinobacteria and Firmicutes. The leakage of Ralstonia and Actinobacteria was probably due to their small sizes judging from microscopic observation, while a longer filtration time is needed for Methylobacterium and Methylorubrum to be detected in the filtrate.